Variant report

Variant	rs1447993
Chromosome Location	chr4:87857591-87857592
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr4:87856979-87857995	GM12878	blood:	n/a	n/a
2	TCF7L2	chr4:87857182-87857987	PANC-1	pancreas:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
3	POLR2A	chr4:87857053-87857763	GM12892	blood:	n/a	n/a
4	POLR2A	chr4:87855558-87857751	HUVEC	blood vessel:	n/a	n/a
5	CTCF	chr4:87857580-87857730	GM12871	blood:	n/a	n/a
6	RAD21	chr4:87857484-87857813	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:87855390-87857870	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:87857126-87857641	PANC-1	pancreas:	n/a	n/a
9	JUND	chr4:87857117-87857657	Hela-S3	cervix:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857424-87857433 chr4:87857422-87857433
10	POLR2A	chr4:87855746-87857756	GM12878	blood:	n/a	n/a
11	MYC	chr4:87857130-87857592	MCF10A-Er-Src	breast:	n/a	n/a
12	CUX1	chr4:87857125-87858337	K562	blood:	n/a	n/a
13	MAZ	chr4:87857118-87857836	HepG2	liver:	n/a	n/a
14	HEY1	chr4:87856963-87857791	HepG2	liver:	n/a	n/a
15	CTCF	chr4:87857549-87857769	GM12892	blood:	n/a	n/a
16	CREB1	chr4:87856798-87857965	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:87855397-87857921	GM19099	blood:	n/a	n/a
18	TCF7L2	chr4:87856233-87857994	Hela-S3	cervix:	n/a	chr4:87857812-87857826 chr4:87857815-87857824 chr4:87857424-87857433
19	HNF4G	chr4:87857352-87857915	HepG2	liver:	n/a	chr4:87857707-87857719 chr4:87857706-87857721 chr4:87857707-87857719 chr4:87857705-87857720 chr4:87857706-87857720
20	CTCF	chr4:87857560-87857710	GM12870	blood:	n/a	n/a
21	HCFC1	chr4:87855249-87857912	K562	blood:	n/a	n/a
22	FOS	chr4:87856947-87857592	MCF10A-Er-Src	breast:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857422-87857433 chr4:87857424-87857433
23	SMC3	chr4:87856810-87857825	Hela-S3	cervix:	n/a	n/a
24	BATF	chr4:87856994-87857773	GM12878	blood:	n/a	chr4:87857425-87857435
25	ZNF384	chr4:87857130-87858070	K562	blood:	n/a	n/a
26	SIN3A	chr4:87857054-87857961	GM12878	blood:	n/a	n/a
27	POLR2A	chr4:87856760-87857737	HCT-116	colon:	n/a	n/a
28	CTCF	chr4:87857520-87857670	GM12873	blood:	n/a	n/a
29	CTCF	chr4:87857307-87857867	K562	blood:	n/a	n/a
30	HDAC2	chr4:87857360-87858017	HepG2	liver:	n/a	chr4:87857728-87857742
31	POLR2A	chr4:87855314-87857869	NB4	blood:	n/a	n/a
32	CEBPB	chr4:87856536-87857732	K562	blood:	n/a	n/a
33	SP1	chr4:87857148-87857979	A549	lung:	n/a	n/a
34	POLR2A	chr4:87856064-87857845	HepG2	liver:	n/a	n/a
35	POLR2A	chr4:87855525-87857861	GM12892	blood:	n/a	n/a
36	CTCF	chr4:87857059-87857853	GM12878	blood:	n/a	n/a
37	FOS	chr4:87856952-87857607	MCF10A-Er-Src	breast:	n/a	chr4:87857423-87857432 chr4:87857427-87857435 chr4:87857422-87857433 chr4:87857424-87857433
38	MAFK	chr4:87857088-87857901	HepG2	liver:	n/a	n/a
39	POLR2A	chr4:87855410-87857773	GM12878	blood:	n/a	n/a
40	ZNF143	chr4:87856676-87857887	GM12878	blood:	n/a	n/a
41	POLR2A	chr4:87855428-87858463	MCF10A-Er-Src	breast:	n/a	n/a
42	RAD21	chr4:87857336-87857906	GM12878	blood:	n/a	n/a
43	RAD21	chr4:87857378-87857781	K562	blood:	n/a	n/a
44	POLR2A	chr4:87855256-87857801	K562	blood:	n/a	n/a
45	POLR2A	chr4:87856732-87857694	HCT-116	colon:	n/a	n/a
46	SMC3	chr4:87857111-87857982	GM12878	blood:	n/a	n/a
47	CEBPD	chr4:87855264-87857762	K562	blood:	n/a	n/a
48	STAT3	chr4:87857206-87857598	MCF10A-Er-Src	breast:	n/a	n/a
49	EP300	chr4:87857176-87857994	HepG2	liver:	n/a	chr4:87857855-87857862
50	CEBPB	chr4:87857084-87858012	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:87855388..87857616-chr4:87927379..87929131,8	MCF-7	breast:
2	chr4:87845889..87863516-chr4:87925389..87935181,79	K562	blood:
3	chr4:87853595..87871697-chr4:87924007..87941983,77	K562	blood:
4	chr4:87853395..87861870-chr4:87925425..87930611,18	MCF-7	breast:
5	chr4:87854708..87860113-chr4:87926348..87930107,23	MCF-7	breast:

Variant related genes	Relation type
C4orf36	TF binding region
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12506662	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17012186	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs1868246	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1992876	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap]
rs2442078	0.86[EUR][1000 genomes]
rs2705621	0.88[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs2869632	0.92[CHB][hapmap]
rs2904151	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs3775229	0.82[CHD][hapmap]
rs3775230	0.86[CHD][hapmap]
rs6419117	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6836128	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs725030	0.92[CHB][hapmap];0.89[CHD][hapmap]
rs72613148	0.92[EUR][1000 genomes]
rs72613149	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657530	0.82[YRI][hapmap]
rs7671931	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9996533	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv508297	chr4:87778783-87868508	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	esv3421759	chr4:87855153-87857701	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1447993	HERC6	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87854800-87858600	Active TSS	Right Ventricle	heart
2	chr4:87854800-87859200	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr4:87855000-87857800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:87855000-87857800	Active TSS	Brain Angular Gyrus	brain
5	chr4:87855000-87858000	Active TSS	Duodenum Mucosa	Duodenum
6	chr4:87855000-87858000	Active TSS	HMEC	breast
7	chr4:87855000-87858200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr4:87855000-87858400	Active TSS	H9 Cell Line	embryonic stem cell
9	chr4:87855000-87858400	Active TSS	Psoas Muscle	Psoas
10	chr4:87855000-87859000	Active TSS	Colonic Mucosa	Colon
11	chr4:87855000-87859000	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr4:87855000-87859800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:87855200-87857600	Active TSS	Colon Smooth Muscle	Colon
14	chr4:87855200-87857600	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:87855200-87857600	Active TSS	NHDF-Ad	bronchial
16	chr4:87855200-87857800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:87855200-87857800	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr4:87855200-87857800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:87855200-87857800	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr4:87855200-87857800	Active TSS	Left Ventricle	heart
21	chr4:87855200-87857800	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr4:87855200-87858200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr4:87855200-87858200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:87855200-87858200	Active TSS	Brain Hippocampus Middle	brain
25	chr4:87855200-87858200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:87855200-87858200	Active TSS	A549	lung
27	chr4:87855200-87858400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:87855200-87858400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr4:87855200-87858600	Active TSS	Stomach Mucosa	stomach
30	chr4:87855200-87859000	Active TSS	Fetal Intestine Large	intestine
31	chr4:87855200-87859200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:87855200-87859200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr4:87855200-87859800	Active TSS	GM12878-XiMat	blood
34	chr4:87855200-87859800	Active TSS	Hela-S3	cervix
35	chr4:87855400-87857600	Active TSS	Small Intestine	intestine
36	chr4:87855400-87857800	Active TSS	Esophagus	oesophagus
37	chr4:87855400-87857800	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr4:87855400-87857800	Active TSS	Gastric	stomach
39	chr4:87855400-87857800	Active TSS	Lung	lung
40	chr4:87855400-87857800	Active TSS	Pancreas	Pancrea
41	chr4:87855400-87858000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr4:87855400-87858000	Active TSS	Rectal Smooth Muscle	rectum
43	chr4:87855400-87858200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:87855400-87858200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:87855400-87858400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:87855400-87858400	Active TSS	Fetal Kidney	kidney
47	chr4:87855400-87859000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:87855400-87859200	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr4:87855400-87859800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr4:87855400-87859800	Active TSS	HUES64 Cell Line	embryonic stem cell

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